If you change too much the hardware of the Crazyflie you will need different tuning of the controller, Crazyswarm is handling that by setting up the controller parameters during connection. the Crazyflie client currently does not have this functionality: if you need different controller configuration when using the Crazyflie client you have to set them manually in the parameter tab or to compile the crazyflie firmware with default values that fits your hardware.

That said, the Qualisys tab currently uses the PID controller that is pretty resilient to noise and hardware change, so it is likely that your modified Crazyflie will fly well out of the box.